Contacts of the helix formed by residues 178 - 188 (chain K) in PDB entry 5G04
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 178 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176K LEU 3.3 2.2 + - - -
177K THR* 1.3 76.7 - - - +
179K GLN* 1.3 60.8 + - - +
180K GLU 3.3 1.3 - - - -
181K GLU* 3.2 43.3 + - - +
182K LYS* 3.4 8.0 + - - +
209K LEU 5.9 0.4 - - - +
212K TYR* 5.8 6.7 - - + -
366K GLY* 4.2 10.6 - - - +
397K ILE* 5.7 7.6 - - + -
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Residues in contact with GLN 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177K THR* 2.7 18.0 + - - +
178K ALA* 1.3 70.1 - - - +
180K GLU* 1.3 83.4 + - - +
182K LYS* 3.4 13.3 + - + +
183K GLU* 3.2 24.2 + - + +
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Residues in contact with GLU 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176K LEU* 3.2 33.6 + - + +
177K THR* 3.5 18.4 + - - +
178K ALA 3.3 0.6 - - - -
179K GLN* 1.3 87.4 - - - +
181K GLU* 1.3 54.7 + - - +
183K GLU* 2.9 25.8 + - - +
184K LEU* 2.4 42.2 + - + +
365K LYS* 5.6 1.9 + - - +
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Residues in contact with GLU 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K THR* 5.0 0.4 - - - -
175K MET 3.1 19.5 - - - +
176K LEU* 3.6 23.9 - - + +
178K ALA* 3.2 35.6 + - - +
180K GLU* 1.3 77.5 - - - +
182K LYS* 1.3 56.7 + - - +
184K LEU* 3.7 7.6 - - - +
185K LEU* 2.9 25.6 + - - +
209K LEU* 3.2 67.5 - - + +
211K LYS* 3.8 13.7 + - - -
366K GLY* 4.7 1.9 - - - -
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Residues in contact with LYS 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178K ALA 3.4 6.7 + - - +
179K GLN* 3.4 14.1 + - + +
180K GLU 3.2 0.6 - - - -
181K GLU* 1.3 78.4 - - - +
183K GLU* 1.3 68.9 + - + +
185K LEU* 3.4 5.2 + - - +
186K GLU* 3.1 56.8 + - + +
209K LEU* 4.7 2.7 - - - +
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Residues in contact with GLU 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K LYS* 4.4 17.7 + - - -
179K GLN* 3.2 15.2 + - + +
180K GLU* 2.9 33.7 + - - +
182K LYS* 1.3 85.2 - - + +
184K LEU* 1.3 52.5 + - - +
186K GLU* 3.3 12.9 + - - +
187K SER* 2.7 40.1 + - - -
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Residues in contact with LEU 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K LYS* 3.7 45.1 - - + +
157K LEU* 5.2 10.3 - - + -
158K LYS* 5.7 4.3 - - + -
167K PHE* 6.1 4.9 - - + -
170K LEU* 4.1 22.2 - - + -
176K LEU* 4.6 17.3 - - + -
180K GLU* 2.4 32.2 + - + +
181K GLU* 3.7 9.2 - - - +
183K GLU* 1.3 72.6 - - - +
185K LEU* 1.3 62.5 + - + +
187K SER* 3.1 9.2 + - - +
188K LEU* 2.8 39.3 + - + +
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Residues in contact with LEU 185 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167K PHE* 3.8 16.6 - - + -
181K GLU 2.9 13.7 + - - +
182K LYS* 3.9 4.7 - - - +
184K LEU* 1.3 76.6 - - + +
186K GLU* 1.3 63.1 + - + +
188K LEU* 3.3 33.0 + - + +
190K LEU* 4.6 11.1 - - + +
202K ARG* 4.7 11.0 - - + +
205K PHE* 3.5 42.2 - - + -
206K GLU* 3.8 22.7 - - - +
209K LEU* 3.7 24.2 - - + -
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Residues in contact with GLU 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K LYS* 3.1 53.5 + - + +
183K GLU* 3.6 10.5 - - - +
185K LEU* 1.3 77.4 - - + +
187K SER* 1.3 59.4 + - - +
188K LEU 3.2 8.7 - - - +
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Residues in contact with SER 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K LYS* 4.2 8.1 + - - -
158K LYS* 3.8 26.1 + - - +
183K GLU* 2.7 25.8 + - - -
184K LEU* 3.3 14.4 - - - -
186K GLU* 1.3 69.3 - - - +
188K LEU* 1.3 65.1 + - - +
189K PRO* 3.5 4.7 - - - +
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Residues in contact with LEU 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K LEU* 4.7 20.6 - - + +
158K LYS* 4.9 8.0 - - + +
161K VAL* 3.7 34.5 - - + -
167K PHE* 5.9 2.9 - - + -
184K LEU* 2.8 49.3 + - + +
185K LEU* 3.3 35.3 - - + +
186K GLU 3.2 10.6 - - - +
187K SER* 1.3 76.6 - - - +
189K PRO* 1.4 76.5 - - + +
190K LEU* 3.4 18.2 + - + +
205K PHE* 4.7 12.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il